Seagrass restoration might contribute to climate change mitigation efforts by restoring carbon sequestration capacity where it has been lost. However, there have been few empirical investigations into the rate and magnitude of changes in sediment organic carbon stock following seagrass restoration. This study aims to compare patterns of sediment organic carbon stock in the early stages after restoration (6 months, 2 years, 2.5 years, and 5 years) of the seagrass Posidonia australis with adjacent unvegetated sand and continuously vegetated seagrass in Shark Bay, Western Australia. Sediment carbon stock in all restored areas were not significantly different from unvegetated sand, regardless of age. Organic carbon concentrations in surface sediments were similar throughout the top 3 cm. In addition, δ13C of organic carbon of sediment from newly restored seagrass meadows was not significantly different from δ13C of organic carbon from unvegetated sediment. These results indicate that carbon sequestration capacity had not returned up to 5 years after restoration. There is increasing evidence that sediment carbon stocks show little recovery in the early stages of restoration and can take >5 years to return to quantities expected from seagrass meadows.